This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. A two-step proteomics approach was applied to detect low levels of MHC class II peptides from HIV-gag p24 processed by dendritic cells. In the first step MS1 data was obtained for the enriched MHC class II peptides, and the mass chromatograms for the isotope distribution of all possible MHC class II peptides from HIV-gag p24 were visualized. In the second step, the peptides that were detected in step one (i.e. had correct mass and isotope distribution) were targeted for MS/MS analysis. This method allows targeting a large number of peptides (>1000).